GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Shewanella sp. ANA-3

Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 7023927 Shewana3_1139 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)

Query= BRENDA::P00561
         (820 letters)



>FitnessBrowser__ANA3:7023927
          Length = 822

 Score =  919 bits (2374), Expect = 0.0
 Identities = 476/821 (57%), Positives = 595/821 (72%), Gaps = 10/821 (1%)

Query: 1   MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60
           M+V+KFGGTS+AN +RF   ADI+   A+   VATVLSAPA +TN L+ M++  + G+D 
Sbjct: 1   MKVMKFGGTSLANWQRFSMAADIVAKAAKAEPVATVLSAPATVTNALLEMVDVAVKGEDY 60

Query: 61  LPNISDAERIFAELL-----TGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCP 115
            P I   ER+F  L      +GL+++Q     A L      + A+ +  L GI+LL +CP
Sbjct: 61  SPVIQHVERVFTSLYQDAVSSGLSSSQSEVLFAGLSV----QLARWQDRLRGITLLQECP 116

Query: 116 DSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIA 175
           D + A ++  GE++S A+M  V+ A+G     +DP E  L  G  LES VDIA S  R  
Sbjct: 117 DGVRAEIVVAGERLSAALMEQVMLAKGITSAQLDPRELFLGRGRPLESVVDIAVSKPRFK 176

Query: 176 ASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTC 235
              +    + +M GFTA +E G++V LGRNGSDYSAAVLAACL A  CEIWTDVDGVY  
Sbjct: 177 NLALDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNT 236

Query: 236 DPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLI 295
           DPR V DA+LL  +SYQEAMELSYFGAKVLHP+TI PIAQF IPC IKN+ NP APGTL+
Sbjct: 237 DPRVVTDAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLV 296

Query: 296 GASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSE 355
               DE  L VK ISNL+N  MF VSGPGMKGMVGMA+R  AA+SR+ +SV LITQSS E
Sbjct: 297 SNQADESGLQVKAISNLDNQTMFDVSGPGMKGMVGMASRTLAAISRSGVSVSLITQSSCE 356

Query: 356 YSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAK 415
           YSISFCV  SD  + + A+++EF LE+K  LLEP+ +   LAI+S++GDGMRT +G++A+
Sbjct: 357 YSISFCVATSDAAKVKSALEQEFELEIKSDLLEPIEMRHDLAIVSLIGDGMRTHKGVAAR 416

Query: 416 FFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGG 475
           FF ALA+A++NI+AIAQGSSERSIS V+        V   HQ  F+  Q ++VF++G G 
Sbjct: 417 FFQALAQASVNIIAIAQGSSERSISTVIEQRKTKHAVAACHQGFFDVQQYLDVFLVGCGN 476

Query: 476 VGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLG 535
           VG  LLEQ+K Q S LK +HI +RVCG+ NS  +L +  G++L NWQ  LA +++P +L 
Sbjct: 477 VGAGLLEQIKHQASVLKEQHISIRVCGIVNSSKMLLDSAGIDLNNWQNLLADSQQPSDLS 536

Query: 536 RLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYA 595
            L+  VKE  LLNPV+VDCTSS  V++QY + +  G HVVTPNKKANT    YY  LR  
Sbjct: 537 ALLAWVKEQQLLNPVLVDCTSSDQVSNQYLEVMNAGMHVVTPNKKANTRDYAYYQALRQT 596

Query: 596 AEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSE 655
           A K RR+FLY+TNVGAGLPVI+NL+ LL AGD+L KF+GILSGSLS+IFGKLDEGM+ SE
Sbjct: 597 ALKQRRQFLYETNVGAGLPVIDNLKKLLFAGDKLHKFNGILSGSLSFIFGKLDEGMTLSE 656

Query: 656 ATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDV 715
           AT LARE  +TEPDPRDDLSGMDVARK+LILARE G +LEL+DI ++ VLP +F+  GDV
Sbjct: 657 ATKLAREKCFTEPDPRDDLSGMDVARKVLILAREVGLKLELSDIVVDSVLPDDFDDSGDV 716

Query: 716 AAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGE 775
            +FMA L++ D   AARVA+A+ +GKVLRYVG I E+G C V+I EVD  DPL+ VK GE
Sbjct: 717 ESFMARLTEADAAIAARVAEAKAQGKVLRYVGQI-EEGACYVRITEVDATDPLYSVKGGE 775

Query: 776 NALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816
           NALAFYS YYQP+P VLRGYGAG +VTAAG FAD+LRTL+W
Sbjct: 776 NALAFYSRYYQPIPFVLRGYGAGTEVTAAGAFADVLRTLNW 816


Lambda     K      H
   0.319    0.135    0.384 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1487
Number of extensions: 53
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 820
Length of database: 822
Length adjustment: 42
Effective length of query: 778
Effective length of database: 780
Effective search space:   606840
Effective search space used:   606840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)

Align candidate 7023927 Shewana3_1139 (bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq))
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00657.hmm
# target sequence database:        /tmp/gapView.10778.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00657  [M=442]
Accession:   TIGR00657
Description: asp_kinases: aspartate kinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.8e-129  418.6   0.4   2.3e-129  418.2   0.4    1.1  1  lcl|FitnessBrowser__ANA3:7023927  Shewana3_1139 bifunctional aspar


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023927  Shewana3_1139 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.2   0.4  2.3e-129  2.3e-129       5     441 ..       3     461 ..       1     462 [. 0.92

  Alignments for each domain:
  == domain 1  score: 418.2 bits;  conditional E-value: 2.3e-129
                         TIGR00657   5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee....keliekirekhleal 77 
                                       V+KFGGtS++n +r++ +a+iv k+++ + +v++V+SA+a vT+aL+e+++ + ++e+     + +e+++++ ++ +
  lcl|FitnessBrowser__ANA3:7023927   3 VMKFGGTSLANWQRFSMAADIVAKAAKAE-PVATVLSAPATVTNALLEMVDVAVKGEDyspvIQHVERVFTSLYQDA 78 
                                       9************************9666.**********************9999998666566666666665555 PP

                         TIGR00657  78 eela.sqalkeklkallekeleevkk...............ereldlilsvGEklSaallaaaleelgvkavsllga 138
                                        +   s   + +++ l +   +++ +               +  +++i+  GE+lSaal+ +++ ++g+ +++ l++
  lcl|FitnessBrowser__ANA3:7023927  79 VSSGlS---SSQSEVLFAGLSVQLARwqdrlrgitllqecpDGVRAEIVVAGERLSAALMEQVMLAKGITSAQ-LDP 151
                                       444444...455555555555555555669999***********************************76665.699 PP

                         TIGR00657 139 eagiltdsefgrAkvleeikterlek.lleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiyt 214
                                       ++  l  ++ ++++v + +++ r ++ +l+e+ + v+ GF++a+e+g+++tLGR+GSD++Aa+lAa+l+A+ +ei+t
  lcl|FitnessBrowser__ANA3:7023927 152 RELFLGRGRPLESVVDIAVSKPRFKNlALDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWT 228
                                       9999**********888888887766268999********************************************* PP

                         TIGR00657 215 DVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseee 291
                                       DVdG+y +DPr+v +A++l ++sy+Ea+EL+++GakvLhp+t+ p++++ ip+ +k++fnp+a+GTl+ ++ + e+ 
  lcl|FitnessBrowser__ANA3:7023927 229 DVDGVYNTDPRVVTDAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLVSNQAD-ESG 304
                                       ***********************************************************************98.666 PP

                         TIGR00657 292 pavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk...kk 363
                                        +vka+s+ +nq++++vsg++mk  +g++++ + a+++ +v+v li+qss e+sisf+v ++da k k++l+   + 
  lcl|FitnessBrowser__ANA3:7023927 305 LQVKAISNLDNQTMFDVSGPGMKgmVGMASRTLAAISRSGVSVSLITQSSCEYSISFCVATSDAAKVKSALEqefEL 381
                                       **********************************************************************9977777 PP

                         TIGR00657 364 vkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealhe 438
                                       + + + le++e+ ++la+vsl+G+gm++++gvaa++f+aLa++ +ni +i+  sse++is+v+++++ ++av a h+
  lcl|FitnessBrowser__ANA3:7023927 382 EIKSDLLEPIEMRHDLAIVSLIGDGMRTHKGVAARFFQALAQASVNIIAIAqgSSERSISTVIEQRKTKHAVAACHQ 458
                                       88999************************************************************************ PP

                         TIGR00657 439 klv 441
                                        ++
  lcl|FitnessBrowser__ANA3:7023927 459 GFF 461
                                       987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (822 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.89
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory